1 SCI comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-8 vs. 2e-6).

The Casal2 ADOL-C and BetaDiff low tolerance models have the same tolerance values than the CASAL base model (1e-8 vs. 2e-6).

1.1 SCI model characteristics

The main characteristics of the Test Case SCI (Scampi) CASAL model are:

  • length-based sex-specific model
  • years 1986 - 2022, projection years 2023 - 2027
  • three time steps, Oct - Jan, Feb - Apr, May - Sep
  • estimate growth transition matrix
  • dour tag releases
  • Beverton-Holt stock-recruitment relationship, with steepness (h) 0.75 and \(CV_R\) 0.7 (prior)
  • length-weight relationship (\(W = aL^b\))
  • three fisheries

Observation data include:

  • trawl fishery CPUE
  • trawl survey abundance and proportions-at-length
  • fishery proportions-at-length
  • tag-recapture data for growth estimation
  • maturity data

Parameters estimated include:

  • B0
  • sex-specific growth parameters
  • maturity parameters
  • YCS (recruitment deviations)
  • sex-specific fishery and trawl selectivity parameters

1.2 R environment

## [1] "Wed Aug 17 16:41:45 2022"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Casal2_22.08   casal_2.30     devtools_2.4.4 usethis_2.1.6  rlist_0.4.6.2 
##  [6] ggthemes_4.2.4 gridExtra_2.3  coda_0.19-4    ggmcmc_1.5.1.1 ggplot2_3.3.6 
## [11] tidyr_1.2.0    huxtable_5.5.0 dplyr_1.0.9    plyr_1.8.7    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9         lattice_0.20-38    prettyunits_1.1.1  ps_1.7.1          
##  [5] assertthat_0.2.1   digest_0.6.29      utf8_1.2.2         mime_0.12         
##  [9] R6_2.5.1           evaluate_0.16      pillar_1.8.0       rlang_1.0.4       
## [13] rstudioapi_0.13    data.table_1.14.2  miniUI_0.1.1.1     urlchecker_1.0.1  
## [17] callr_3.7.1        jquerylib_0.1.4    rmarkdown_2.15     stringr_1.4.0     
## [21] htmlwidgets_1.5.4  munsell_0.5.0      shiny_1.7.2        compiler_3.6.0    
## [25] httpuv_1.6.5       xfun_0.32          pkgconfig_2.0.3    pkgbuild_1.3.1    
## [29] htmltools_0.5.3    tidyselect_1.1.2   tibble_3.1.8       reshape_0.8.9     
## [33] fansi_1.0.3        crayon_1.5.1       withr_2.5.0        later_1.3.0       
## [37] grid_3.6.0         jsonlite_1.8.0     xtable_1.8-4       GGally_2.1.2      
## [41] gtable_0.3.0       lifecycle_1.0.1    DBI_1.1.3          magrittr_2.0.3    
## [45] scales_1.2.0       cli_3.3.0          stringi_1.7.8      cachem_1.0.6      
## [49] remotes_2.4.2      fs_1.5.2           promises_1.2.0.1   bslib_0.4.0       
## [53] ellipsis_0.3.2     generics_0.1.3     vctrs_0.4.1        RColorBrewer_1.1-3
## [57] tools_3.6.0        glue_1.6.2         purrr_0.3.4        pkgload_1.3.0     
## [61] processx_3.7.0     fastmap_1.1.0      yaml_2.3.5         colorspace_2.0-3  
## [65] sessioninfo_1.2.2  memoise_2.0.1      knitr_1.39         profvis_0.3.7     
## [69] sass_0.4.2

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates
rownamesBase_ModelSensitivity_1Percent_Diff
initialization.B0           2106.000002106.000000.000
growth[1].minsigma_male4.519004.519000.000
recruitment.YCS1         0.261000.261000.000
recruitment.YCS2         0.281900.281900.000
recruitment.YCS3         0.353700.353700.000
recruitment.YCS4         0.549400.549400.000
recruitment.YCS5         3.080003.080000.000
recruitment.YCS6         0.615700.615700.000
recruitment.YCS7         0.600200.600200.000
recruitment.YCS8         0.506300.506300.000
recruitment.YCS9         0.314600.314600.000
recruitment.YCS10        0.385500.385500.000
recruitment.YCS11        0.396800.396800.000
recruitment.YCS12        0.372700.372700.000
recruitment.YCS13        0.498900.498900.000
recruitment.YCS14        0.375300.375300.000
recruitment.YCS15        0.499400.499400.000
recruitment.YCS16        0.535200.535200.000
recruitment.YCS17        0.593400.593400.000
recruitment.YCS18        0.365600.365600.000
recruitment.YCS19        0.599200.599200.000
recruitment.YCS20        0.464200.464200.000
recruitment.YCS21        0.493900.493900.000
recruitment.YCS22        0.551300.551300.000
recruitment.YCS23        0.987500.987500.000
recruitment.YCS24        0.530800.530800.000
recruitment.YCS25        0.885400.885400.000
recruitment.YCS26        0.913100.913100.000
recruitment.YCS27        0.511600.511600.000
recruitment.YCS28        0.642900.642900.000
recruitment.YCS29        0.449800.44990-0.022
recruitment.YCS30        0.627600.627600.000
recruitment.YCS31        0.581500.581500.000
recruitment.YCS32        0.555600.555500.018
recruitment.YCS33        0.938700.938700.000
recruitment.YCS34        1.417001.417000.000
recruitment.YCS35        0.393400.393400.000
recruitment.YCS36        0.479000.479000.000
recruitment.YCS37        0.549900.549800.018
maturity_props.all1         30.1200030.120000.000
maturity_props.all2         7.093007.093000.000
selectivity[FishingSel_1].female1      43.9200043.920000.000
selectivity[FishingSel_1].female2      16.3700016.370000.000
selectivity[FishingSel_1].female3      0.855200.855200.000
selectivity[FishingSel_1].female4      1.000001.000000.000
selectivity[FishingSel_2].female1      45.4300045.430000.000
selectivity[FishingSel_2].female2      20.0200020.020000.000
selectivity[FishingSel_2].female3      0.506600.506600.000
selectivity[FishingSel_2].female4      1.000001.000000.000
selectivity[TrawlSurveySel_1].female1      30.6900030.690000.000
selectivity[TrawlSurveySel_1].female2      20.7700020.770000.000
selectivity[TrawlSurveySel_1].female3      1.129001.129000.000
selectivity[TrawlSurveySel_1].female4      1.000001.000000.000
selectivity[TrawlSurveySel_2].female1      36.9800036.980000.000
selectivity[TrawlSurveySel_2].female2      16.9400016.940000.000
selectivity[TrawlSurveySel_2].female3      1.087001.087000.000
selectivity[TrawlSurveySel_2].female4      1.000001.000000.000
growth[1].g_male1      13.8600013.860000.000
growth[1].g_male2      2.847002.847000.000
growth[1].g_female1    13.4200013.420000.000
growth[1].g_female2    0.924900.924900.000
Casal2 parameter estimates
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tol
process[Recruitment].b0              2105.510002107.570002105.51000
growth_increment[female_growth].min_sigma       4.518844.596664.51885
process[Recruitment].ycs_values{1985}0.261030.260610.26104
process[Recruitment].ycs_values{1986}0.281880.281340.28188
process[Recruitment].ycs_values{1987}0.353650.350040.35365
process[Recruitment].ycs_values{1988}0.549470.529440.54944
process[Recruitment].ycs_values{1989}3.079923.148723.07993
process[Recruitment].ycs_values{1990}0.615960.609630.61598
process[Recruitment].ycs_values{1991}0.600210.594000.60020
process[Recruitment].ycs_values{1992}0.506280.503650.50628
process[Recruitment].ycs_values{1993}0.314650.315390.31465
process[Recruitment].ycs_values{1994}0.385490.381730.38549
process[Recruitment].ycs_values{1995}0.396780.398960.39678
process[Recruitment].ycs_values{1996}0.372690.374130.37269
process[Recruitment].ycs_values{1997}0.498900.499860.49890
process[Recruitment].ycs_values{1998}0.375300.374260.37530
process[Recruitment].ycs_values{1999}0.499390.501990.49939
process[Recruitment].ycs_values{2000}0.535210.538240.53521
process[Recruitment].ycs_values{2001}0.593340.598000.59334
process[Recruitment].ycs_values{2002}0.365620.364320.36562
process[Recruitment].ycs_values{2003}0.599140.602930.59914
process[Recruitment].ycs_values{2004}0.464220.463580.46423
process[Recruitment].ycs_values{2005}0.493890.494220.49389
process[Recruitment].ycs_values{2006}0.551240.553460.55125
process[Recruitment].ycs_values{2007}0.987450.996900.98745
process[Recruitment].ycs_values{2008}0.530790.532900.53080
process[Recruitment].ycs_values{2009}0.885370.884130.88537
process[Recruitment].ycs_values{2010}0.913110.926240.91312
process[Recruitment].ycs_values{2011}0.511600.504370.51161
process[Recruitment].ycs_values{2012}0.642870.647130.64286
process[Recruitment].ycs_values{2013}0.449840.452720.44985
process[Recruitment].ycs_values{2014}0.627630.624660.62761
process[Recruitment].ycs_values{2015}0.581530.582550.58154
process[Recruitment].ycs_values{2016}0.555540.557940.55554
process[Recruitment].ycs_values{2017}0.938760.941120.93875
process[Recruitment].ycs_values{2018}1.417061.433031.41707
process[Recruitment].ycs_values{2019}0.393400.388990.39339
process[Recruitment].ycs_values{2020}0.478980.478100.47900
process[Recruitment].ycs_values{2021}0.549890.549860.54982
selectivity[maturity].a50             30.1166030.1166030.11660
selectivity[maturity].ato95           7.093057.093057.09305
selectivity[FishingSel_1_male].a50             43.9218044.2195043.92180
selectivity[FishingSel_1_male].ato95           16.3696016.5275016.36950
selectivity[FishingSel_1_male].alpha           0.855180.854240.85518
selectivity[FishingSel_2_female].a50             45.4297045.7797045.42960
selectivity[FishingSel_2_female].ato95           20.0232020.1815020.02320
selectivity[FishingSel_2_male].alpha           0.506610.506480.50662
selectivity[TrawlSurveySel_1_female].a50             30.6937031.0040030.69360
selectivity[TrawlSurveySel_1_female].ato95           20.7706021.7416020.77030
selectivity[TrawlSurveySel_1_male].alpha           1.128771.127481.12876
selectivity[TrawlSurveySel_2_female].a50             36.9843037.2238036.98430
selectivity[TrawlSurveySel_2_female].ato95           16.9428017.1871016.94280
selectivity[TrawlSurveySel_2_male].alpha           1.086871.086651.08687
growth_increment[male_growth].g_alpha         13.8569013.8385013.85690
growth_increment[male_growth].g_beta          2.846802.748532.84680
growth_increment[female_growth].g_alpha         13.4224013.4264013.42240
growth_increment[female_growth].g_beta          0.925080.803580.92508
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tol
process[Recruitment].b0              0.000-0.0980.000
growth_increment[female_growth].min_sigma       0.000-1.722-0.000
process[Recruitment].ycs_values{1985}0.0000.161-0.003
process[Recruitment].ycs_values{1986}0.0000.191-0.001
process[Recruitment].ycs_values{1987}0.0001.0230.001
process[Recruitment].ycs_values{1988}0.0003.6460.005
process[Recruitment].ycs_values{1989}0.000-2.234-0.000
process[Recruitment].ycs_values{1990}0.0001.028-0.003
process[Recruitment].ycs_values{1991}0.0001.0330.001
process[Recruitment].ycs_values{1992}0.0000.518-0.000
process[Recruitment].ycs_values{1993}0.000-0.238-0.001
process[Recruitment].ycs_values{1994}0.0000.9760.001
process[Recruitment].ycs_values{1995}0.000-0.550-0.002
process[Recruitment].ycs_values{1996}0.000-0.3860.001
process[Recruitment].ycs_values{1997}0.000-0.192-0.000
process[Recruitment].ycs_values{1998}0.0000.277-0.001
process[Recruitment].ycs_values{1999}0.000-0.521-0.001
process[Recruitment].ycs_values{2000}0.000-0.5670.000
process[Recruitment].ycs_values{2001}0.000-0.786-0.000
process[Recruitment].ycs_values{2002}0.0000.356-0.001
process[Recruitment].ycs_values{2003}0.000-0.6310.001
process[Recruitment].ycs_values{2004}0.0000.140-0.001
process[Recruitment].ycs_values{2005}0.000-0.0660.000
process[Recruitment].ycs_values{2006}0.000-0.401-0.000
process[Recruitment].ycs_values{2007}0.000-0.9570.001
process[Recruitment].ycs_values{2008}0.000-0.398-0.002
process[Recruitment].ycs_values{2009}0.0000.1400.000
process[Recruitment].ycs_values{2010}0.000-1.437-0.000
process[Recruitment].ycs_values{2011}0.0001.414-0.001
process[Recruitment].ycs_values{2012}0.000-0.6630.002
process[Recruitment].ycs_values{2013}0.000-0.640-0.004
process[Recruitment].ycs_values{2014}0.0000.4730.002
process[Recruitment].ycs_values{2015}0.000-0.175-0.001
process[Recruitment].ycs_values{2016}0.000-0.4310.000
process[Recruitment].ycs_values{2017}0.000-0.2520.000
process[Recruitment].ycs_values{2018}0.000-1.127-0.001
process[Recruitment].ycs_values{2019}0.0001.1210.003
process[Recruitment].ycs_values{2020}0.0000.183-0.004
process[Recruitment].ycs_values{2021}0.0000.0050.012
selectivity[maturity].a50             0.0000.0000.000
selectivity[maturity].ato95           0.0000.0000.000
selectivity[FishingSel_1_male].a50             0.000-0.6780.000
selectivity[FishingSel_1_male].ato95           0.000-0.9650.001
selectivity[FishingSel_1_male].alpha           0.0000.1100.000
selectivity[FishingSel_2_female].a50             0.000-0.7700.000
selectivity[FishingSel_2_female].ato95           0.000-0.7910.000
selectivity[FishingSel_2_male].alpha           0.0000.027-0.000
selectivity[TrawlSurveySel_1_female].a50             0.000-1.0110.000
selectivity[TrawlSurveySel_1_female].ato95           0.000-4.6750.001
selectivity[TrawlSurveySel_1_male].alpha           0.0000.1140.001
selectivity[TrawlSurveySel_2_female].a50             0.000-0.6480.000
selectivity[TrawlSurveySel_2_female].ato95           0.000-1.4420.000
selectivity[TrawlSurveySel_2_male].alpha           0.0000.0200.000
growth_increment[male_growth].g_alpha         0.0000.1330.000
growth_increment[male_growth].g_beta          0.0003.4520.000
growth_increment[female_growth].g_alpha         0.000-0.0300.000
growth_increment[female_growth].g_beta          0.00013.134-0.000
CASAL objective function component values
ComponentBase_ModelSensitivity_1
CPUE-Trawl_117.23017.230
TrawlSurvey_1-5.390-5.390
TrawlSurvey_215.85015.850
TrawlSurveyProportionAtLength_1675.000675.000
TrawlSurveyProportionAtLength_2878.300878.300
CommercialCatchLength_12022.0002022.000
CommercialCatchLength_21470.0001470.000
CommercialCatchLength_31434.0001434.000
Cryer_Oliver_maturity84.06084.060
1997-recaptures1-131.16031.160
1997-recaptures1-261.74061.740
1997-recaptures2-115.14015.140
1997-recaptures2-234.65034.650
1997-recaptures2-327.94027.940
1997-recaptures3-122.85022.850
1997-recaptures3-265.33065.330
1997-recaptures3-358.95058.950
prior_on_initialization.B07.6527.652
prior_on_growth[1].minsigma_male0.0000.000
prior_on_recruitment.YCS-5.344-5.344
prior_on_maturity_props.all0.0000.000
prior_on_selectivity[FishingSel_1].female0.0000.000
prior_on_selectivity[FishingSel_2].female0.0000.000
prior_on_selectivity[TrawlSurveySel_1].female0.0000.000
prior_on_selectivity[TrawlSurveySel_2].female0.0000.000
prior_on_growth[1].g_male0.0000.000
prior_on_growth[1].g_female0.0000.000
prior_on_q_CPUE-Commercialq_1-6.457-6.457
prior_on_q_TrawlSurveyq_1-2.477-2.477
prior_on_q_TrawlSurveyq_2-2.349-2.349
Penalty_Trawl_1_Catch0.0000.000
Penalty_Trawl_2_Catch0.0000.000
Penalty_Trawl_3_Catch0.0000.000
Total6899.0006899.000
Casal2 objective function component values
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tol
observation->CPUE-Trawl_1->1990                 -2.370-2.374-2.370
observation->CPUE-Trawl_1->1991                 5.5525.5285.552
observation->CPUE-Trawl_1->1992                 -0.556-0.527-0.556
observation->CPUE-Trawl_1->1993                 8.9418.8698.941
observation->CPUE-Trawl_1->1994                 -0.466-0.440-0.466
observation->CPUE-Trawl_1->1995                 5.8545.8195.854
observation->CPUE-Trawl_1->1996                 -2.204-2.208-2.204
observation->CPUE-Trawl_1->1997                 2.8702.8652.870
observation->CPUE-Trawl_1->1998                 -2.241-2.238-2.241
observation->CPUE-Trawl_1->1999                 7.1057.0827.105
observation->CPUE-Trawl_1->2000                 -1.373-1.390-1.373
observation->CPUE-Trawl_1->2001                 -0.310-0.273-0.310
observation->CPUE-Trawl_1->2002                 -0.305-0.342-0.305
observation->CPUE-Trawl_1->2003                 -2.020-2.028-2.020
observation->CPUE-Trawl_1->2004                 1.4951.4901.495
observation->CPUE-Trawl_1->2005                 -0.394-0.396-0.394
observation->CPUE-Trawl_1->2006                 -2.180-2.182-2.180
observation->CPUE-Trawl_1->2007                 -1.392-1.394-1.392
observation->CPUE-Trawl_1->2008                 -1.224-1.231-1.224
observation->CPUE-Trawl_1->2009                 -2.417-2.417-2.417
observation->CPUE-Trawl_1->2010                 -0.496-0.509-0.496
observation->CPUE-Trawl_1->2011                 1.6681.6411.668
observation->CPUE-Trawl_1->2012                 4.9824.9434.982
observation->CPUE-Trawl_1->2013                 2.7702.8032.770
observation->CPUE-Trawl_1->2014                 -0.613-0.606-0.613
observation->CPUE-Trawl_1->2015                 1.2111.2061.211
observation->CPUE-Trawl_1->2016                 2.4682.4782.468
observation->CPUE-Trawl_1->2017                 -0.629-0.633-0.629
observation->CPUE-Trawl_1->2018                 -2.289-2.294-2.289
observation->CPUE-Trawl_1->2019                 -0.259-0.239-0.259
observation->CPUE-Trawl_1->2020                 -1.731-1.729-1.731
observation->CPUE-Trawl_1->2021                 -2.221-2.221-2.221
observation->TrawlSurvey_1->1993                 -1.801-1.799-1.801
observation->TrawlSurvey_1->1994                 -1.820-1.820-1.820
observation->TrawlSurvey_1->1995                 -1.721-1.721-1.721
observation->TrawlSurvey_1->2004                 -0.048-0.038-0.048
observation->TrawlSurvey_2->2003                 -0.491-0.490-0.491
observation->TrawlSurvey_2->2005                 -0.901-0.901-0.901
observation->TrawlSurvey_2->2006                 -0.988-0.988-0.988
observation->TrawlSurvey_2->2012                 8.2068.1978.206
observation->TrawlSurvey_2->2015                 -1.238-1.238-1.238
observation->TrawlSurvey_2->2018                 12.34312.32112.343
observation->TrawlSurvey_2->2021                 -1.079-1.079-1.079
observation->TrawlSurveyProportionAtLength_1->1993                 140.116140.149140.117
observation->TrawlSurveyProportionAtLength_1->1994                 136.075136.211136.075
observation->TrawlSurveyProportionAtLength_1->1995                 134.809134.741134.809
observation->TrawlSurveyProportionAtLength_1->2004                 136.719136.752136.719
observation->TrawlSurveyProportionAtLength_1->2021                 127.242127.234127.242
observation->TrawlSurveyProportionAtLength_2->2003                 122.195122.196122.195
observation->TrawlSurveyProportionAtLength_2->2005                 127.870127.854127.870
observation->TrawlSurveyProportionAtLength_2->2006                 132.110131.974132.110
observation->TrawlSurveyProportionAtLength_2->2012                 131.462131.375131.462
observation->TrawlSurveyProportionAtLength_2->2015                 119.936119.991119.936
observation->TrawlSurveyProportionAtLength_2->2018                 125.164125.341125.164
observation->TrawlSurveyProportionAtLength_2->2021                 119.526119.560119.526
observation->CommercialCatchLength_1->1992                 68.89968.87368.899
observation->CommercialCatchLength_1->1993                 85.87985.72585.879
observation->CommercialCatchLength_1->1996                 147.667147.860147.667
observation->CommercialCatchLength_1->1997                 84.24784.12484.247
observation->CommercialCatchLength_1->1998                 117.490117.428117.490
observation->CommercialCatchLength_1->1999                 139.920139.921139.920
observation->CommercialCatchLength_1->2000                 115.382115.345115.382
observation->CommercialCatchLength_1->2001                 123.573123.520123.573
observation->CommercialCatchLength_1->2002                 94.87794.77794.877
observation->CommercialCatchLength_1->2003                 152.191151.986152.191
observation->CommercialCatchLength_1->2005                 93.31393.19293.313
observation->CommercialCatchLength_1->2008                 154.113154.375154.113
observation->CommercialCatchLength_1->2011                 112.774112.747112.774
observation->CommercialCatchLength_1->2012                 153.745153.501153.745
observation->CommercialCatchLength_1->2013                 109.472109.380109.472
observation->CommercialCatchLength_1->2014                 93.14593.15593.145
observation->CommercialCatchLength_1->2020                 174.821174.725174.821
observation->CommercialCatchLength_2->1994                 101.844101.868101.844
observation->CommercialCatchLength_2->1995                 109.767109.724109.767
observation->CommercialCatchLength_2->1997                 116.900116.834116.900
observation->CommercialCatchLength_2->1998                 155.404156.498155.403
observation->CommercialCatchLength_2->1999                 124.131124.045124.131
observation->CommercialCatchLength_2->2007                 131.024130.931131.024
observation->CommercialCatchLength_2->2008                 158.478158.829158.478
observation->CommercialCatchLength_2->2009                 177.935177.854177.935
observation->CommercialCatchLength_2->2012                 138.105138.672138.105
observation->CommercialCatchLength_2->2019                 141.424141.526141.424
observation->CommercialCatchLength_2->2021                 114.547114.412114.547
observation->CommercialCatchLength_3->1991                 137.377137.256137.377
observation->CommercialCatchLength_3->1993                 90.37290.40490.372
observation->CommercialCatchLength_3->1994                 122.548122.354122.548
observation->CommercialCatchLength_3->1995                 104.971105.142104.971
observation->CommercialCatchLength_3->1996                 82.54382.37482.543
observation->CommercialCatchLength_3->1997                 107.868107.733107.868
observation->CommercialCatchLength_3->2000                 116.229116.227116.229
observation->CommercialCatchLength_3->2001                 179.354178.915179.354
observation->CommercialCatchLength_3->2007                 129.099128.996129.099
observation->CommercialCatchLength_3->2008                 111.241111.297111.241
observation->CommercialCatchLength_3->2010                 138.651138.500138.651
observation->CommercialCatchLength_3->2011                 113.720113.605113.720
observation->Cryer_Oliver_maturity                 84.05784.05784.057
observation->1997_recaptures1_1                 31.16531.18931.165
observation->1997_recaptures1_2                 61.74061.74061.740
observation->1997_recaptures2_1                 15.13615.13315.136
observation->1997_recaptures2_2                 34.64934.63934.649
observation->1997_recaptures2_3                 27.93827.93827.938
observation->1997_recaptures3_1                 22.85122.82122.851
observation->1997_recaptures3_2                 65.32865.49965.328
observation->1997_recaptures3_3                 58.94858.94658.948
prior->B0->process[Recruitment].b0              7.6527.6537.652
prior->growth_min_sigma->growth_increment[female_growth].min_sigma       0.0000.0000.000
prior->YCS->process[Recruitment].ycs_values{1985}0.2970.3000.297
prior->YCS->process[Recruitment].ycs_values{1986}0.1610.1640.161
prior->YCS->process[Recruitment].ycs_values{1987}-0.155-0.143-0.155
prior->YCS->process[Recruitment].ycs_values{1988}-0.399-0.397-0.399
prior->YCS->process[Recruitment].ycs_values{1989}3.3243.4203.324
prior->YCS->process[Recruitment].ycs_values{1990}-0.383-0.385-0.383
prior->YCS->process[Recruitment].ycs_values{1991}-0.389-0.391-0.389
prior->YCS->process[Recruitment].ycs_values{1992}-0.390-0.389-0.390
prior->YCS->process[Recruitment].ycs_values{1993}-0.008-0.011-0.008
prior->YCS->process[Recruitment].ycs_values{1994}-0.241-0.232-0.241
prior->YCS->process[Recruitment].ycs_values{1995}-0.265-0.270-0.265
prior->YCS->process[Recruitment].ycs_values{1996}-0.209-0.213-0.209
prior->YCS->process[Recruitment].ycs_values{1997}-0.387-0.387-0.387
prior->YCS->process[Recruitment].ycs_values{1998}-0.216-0.213-0.216
prior->YCS->process[Recruitment].ycs_values{1999}-0.387-0.388-0.387
prior->YCS->process[Recruitment].ycs_values{2000}-0.398-0.398-0.398
prior->YCS->process[Recruitment].ycs_values{2001}-0.392-0.390-0.392
prior->YCS->process[Recruitment].ycs_values{2002}-0.190-0.186-0.190
prior->YCS->process[Recruitment].ycs_values{2003}-0.390-0.388-0.390
prior->YCS->process[Recruitment].ycs_values{2004}-0.363-0.362-0.363
prior->YCS->process[Recruitment].ycs_values{2005}-0.384-0.385-0.384
prior->YCS->process[Recruitment].ycs_values{2006}-0.399-0.399-0.399
prior->YCS->process[Recruitment].ycs_values{2007}0.0310.0450.031
prior->YCS->process[Recruitment].ycs_values{2008}-0.397-0.398-0.397
prior->YCS->process[Recruitment].ycs_values{2009}-0.114-0.116-0.114
prior->YCS->process[Recruitment].ycs_values{2010}-0.076-0.058-0.076
prior->YCS->process[Recruitment].ycs_values{2011}-0.392-0.389-0.392
prior->YCS->process[Recruitment].ycs_values{2012}-0.368-0.365-0.368
prior->YCS->process[Recruitment].ycs_values{2013}-0.348-0.351-0.348
prior->YCS->process[Recruitment].ycs_values{2014}-0.377-0.378-0.377
prior->YCS->process[Recruitment].ycs_values{2015}-0.395-0.395-0.395
prior->YCS->process[Recruitment].ycs_values{2016}-0.399-0.399-0.399
prior->YCS->process[Recruitment].ycs_values{2017}-0.040-0.037-0.040
prior->YCS->process[Recruitment].ycs_values{2018}0.7250.7520.725
prior->YCS->process[Recruitment].ycs_values{2019}-0.258-0.249-0.258
prior->YCS->process[Recruitment].ycs_values{2020}-0.375-0.374-0.375
prior->YCS->process[Recruitment].ycs_values{2021}-0.399-0.399-0.399
prior->maturity_a50->selectivity[maturity].a50             0.0000.0000.000
prior->maturity_ato95->selectivity[maturity].ato95           0.0000.0000.000
prior->FishingSel_1_a50->selectivity[FishingSel_1_male].a50             0.0000.0000.000
prior->FishingSel_1_ato95->selectivity[FishingSel_1_male].ato95           0.0000.0000.000
prior->FishingSel_1_male_alpha->selectivity[FishingSel_1_male].alpha           0.0000.0000.000
prior->FishingSel_2_a50->selectivity[FishingSel_2_female].a50             0.0000.0000.000
prior->FishingSel_2_ato95->selectivity[FishingSel_2_female].ato95           0.0000.0000.000
prior->FishingSel_2_male_alpha->selectivity[FishingSel_2_male].alpha           0.0000.0000.000
prior->TrawlSurveySel_1_a50->selectivity[TrawlSurveySel_1_female].a50             0.0000.0000.000
prior->TrawlSurveySel_1_ato95->selectivity[TrawlSurveySel_1_female].ato95           0.0000.0000.000
prior->TrawlSurveySel_1_male_alpha->selectivity[TrawlSurveySel_1_male].alpha           0.0000.0000.000
prior->TrawlSurveySel_2_a50->selectivity[TrawlSurveySel_2_female].a50             0.0000.0000.000
prior->TrawlSurveySel_2_ato95->selectivity[TrawlSurveySel_2_female].ato95           0.0000.0000.000
prior->TrawlSurveySel_2_male_alpha->selectivity[TrawlSurveySel_2_male].alpha           0.0000.0000.000
prior->g_alpha_male->growth_increment[male_growth].g_alpha         0.0000.0000.000
prior->g_beta_male->growth_increment[male_growth].g_beta          0.0000.0000.000
prior->g_alpha_female->growth_increment[female_growth].g_alpha         0.0000.0000.000
prior->g_beta_female->growth_increment[female_growth].g_beta          0.0000.0000.000
additional_prior->CPUE-Commercialq_1                 -6.457-6.436-6.457
additional_prior->TrawlSurveyq_1                 -2.477-2.460-2.477
additional_prior->TrawlSurveyq_2                 -2.349-2.336-2.349
total_score                 6898.7906898.7406898.790
## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-06"                                                                   
## [2] "Minimiser achieved convergence after 119 quasi-Newton iterations using 126 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-08"                                                                   
## [2] "Minimiser achieved convergence after 134 quasi-Newton iterations using 153 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.64873e-06 f = 6898.79"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.83524e-06 f = 6898.74"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: have converged: t = 2.30345e-09 f = 6898.79"
## [2] "Successful convergence in optimise"
## [1] "CASAL model warnings"
## NULL
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## NULL
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## [1] ""
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## [1] ""

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 1 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 2 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl 3 match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others…

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.9193 0.9407"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.9193 0.94"

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): -0.919151 0.940771"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.922937 0.943642"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.920111 0.939971"